I was poking around the Paizo website, and noticed that there are minis for Pathfinder, and others for Pathfinder Chronicles. What's the difference between the two? I couldn't see anything in my research.

Pathfinder Player Companion - was: Pathfinder Companion, mostly player-focused guides with additional crunch and player-safe setting info for a given race or country.

Also Tales (novels), Miniatures (minis), and Organized Play (adventure scenarios for tournament play).

A lot of this was somewhat confusing and has undergone a couple revs of rebranding, so when you see "Pathfinder Chronicles Mini" it probably is just a legacy term from before there was a "Pathfinder Minis" line and they were lumped into Chronicles.

Pathfinder Chronicles was simply the Pathfinder RPG Lore content owned by Paizo before Pathfinder was released as a standalone RPG (It was third party material for D&D3.5e). As such, "Chronicles" is often used to refer to this legacy content, at least in the context you're asking about.